Qian Liu
| Snapshot Date: 2025-12-10 13:40 -0500 (Wed, 10 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: 4a5d06b |
| git_last_commit_date: 2025-10-29 11:20:44 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-11 11:35 -0500 (Thu, 11 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4872 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4580 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1753/2331 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.11.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the ReUseData package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ReUseData.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: ReUseData |
| Version: 1.11.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ReUseData_1.11.0.tar.gz |
| StartedAt: 2025-12-11 04:44:47 -0500 (Thu, 11 Dec 2025) |
| EndedAt: 2025-12-11 04:47:35 -0500 (Thu, 11 Dec 2025) |
| EllapsedTime: 168.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ReUseData_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.11.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ReUseData’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dataHub-class 5.992 0.346 6.338
getCloudData 2.844 0.080 5.261
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.11.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ReUseData)
ReUseData.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(ReUseData)
>
> test_check("ReUseData")
Note: you need to assign a name for the recipe: rcpName <- recipeLoad('xx')
Data recipe loaded!
Use inputs() to check required input parameters before evaluation.
Check here: https://rcwl.org/dataRecipes/echo_out.html
for user instructions (e.g., eligible input values, data source, etc.)
}[1;30mINFO[0m Final process status is success
Updating data record...
outfile.txt added
Updating data record...
c6cb43d29d87_GRCh38.primary_assembly.genome.fa.1.bt2 added
c6cb47e064c4c_GRCh38.primary_assembly.genome.fa.2.bt2 added
c6cb4dd1bc76_GRCh38.primary_assembly.genome.fa.3.bt2 added
c6cb4d1b7f8f_GRCh38.primary_assembly.genome.fa.4.bt2 added
c6cb4150dd106_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
c6cb436506426_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
c6cb46c835681_outfile.txt added
c6cb4451d7b3d_GRCh37_to_GRCh38.chain added
c6cb42d2dc62a_GRCh37_to_NCBI34.chain added
c6cb4315571c0_GRCh37_to_NCBI35.chain added
c6cb41e0f1713_GRCh37_to_NCBI36.chain added
c6cb47a026a9a_GRCh38_to_GRCh37.chain added
c6cb44a19755f_GRCh38_to_NCBI34.chain added
c6cb414acc94f_GRCh38_to_NCBI35.chain added
c6cb476d0eeb_GRCh38_to_NCBI36.chain added
c6cb4726ccf62_NCBI34_to_GRCh37.chain added
c6cb47db2e982_NCBI34_to_GRCh38.chain added
c6cb4567a6b82_NCBI35_to_GRCh37.chain added
c6cb4116f59e5_NCBI35_to_GRCh38.chain added
c6cb4732d8282_NCBI36_to_GRCh37.chain added
c6cb496404fa_NCBI36_to_GRCh38.chain added
c6cb414c7291f_GRCm38_to_NCBIM36.chain added
c6cb419607c83_GRCm38_to_NCBIM37.chain added
c6cb451b0e6bd_NCBIM36_to_GRCm38.chain added
c6cb4630a5cde_NCBIM37_to_GRCm38.chain added
c6cb414122a18_1000G_omni2.5.b37.vcf.gz added
c6cb43211c11c_1000G_omni2.5.b37.vcf.gz.tbi added
c6cb45ecd4527_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
c6cb42a1d7006_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
c6cb433fcd7a7_1000G_omni2.5.hg38.vcf.gz added
c6cb45c46b5eb_1000G_omni2.5.hg38.vcf.gz.tbi added
c6cb42df00d8d_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
c6cb4320323f3_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
c6cb46a187261_af-only-gnomad.raw.sites.vcf added
c6cb43b0b8d1c_af-only-gnomad.raw.sites.vcf.idx added
c6cb44710f4f9_Mutect2-exome-panel.vcf.idx added
c6cb42068d687_Mutect2-WGS-panel-b37.vcf added
c6cb4278ee39d_Mutect2-WGS-panel-b37.vcf.idx added
c6cb4c2e7037_small_exac_common_3.vcf added
c6cb44d969cb1_small_exac_common_3.vcf.idx added
c6cb458e4555e_1000g_pon.hg38.vcf.gz added
c6cb42a3d874a_1000g_pon.hg38.vcf.gz.tbi added
c6cb44799074b_af-only-gnomad.hg38.vcf.gz added
c6cb422fdcabd_af-only-gnomad.hg38.vcf.gz.tbi added
c6cb43eea5099_small_exac_common_3.hg38.vcf.gz added
c6cb44f061636_small_exac_common_3.hg38.vcf.gz.tbi added
c6cb4156a9a1f_gencode.v41.annotation.gtf added
c6cb43c9d3a1b_gencode.v42.annotation.gtf added
c6cb4258081b9_gencode.vM30.annotation.gtf added
c6cb426d9f405_gencode.vM31.annotation.gtf added
c6cb42fcabc9d_gencode.v41.transcripts.fa added
c6cb42ee486b3_gencode.v41.transcripts.fa.fai added
c6cb43ba11d24_gencode.v42.transcripts.fa added
c6cb4492b3920_gencode.v42.transcripts.fa.fai added
c6cb4956d70_gencode.vM30.pc_transcripts.fa added
c6cb41eab7a03_gencode.vM30.pc_transcripts.fa.fai added
c6cb45d3d6339_gencode.vM31.pc_transcripts.fa added
c6cb432a72e8d_gencode.vM31.pc_transcripts.fa.fai added
c6cb47d78bf2a_GRCh38.primary_assembly.genome.fa.1.ht2 added
c6cb475ad33f_GRCh38.primary_assembly.genome.fa.2.ht2 added
c6cb466a40634_GRCh38.primary_assembly.genome.fa.3.ht2 added
c6cb459bf7515_GRCh38.primary_assembly.genome.fa.4.ht2 added
c6cb4354ae0cd_GRCh38.primary_assembly.genome.fa.5.ht2 added
c6cb418a72a27_GRCh38.primary_assembly.genome.fa.6.ht2 added
c6cb443d7e776_GRCh38.primary_assembly.genome.fa.7.ht2 added
c6cb470566de9_GRCh38.primary_assembly.genome.fa.8.ht2 added
c6cb45fb81f20_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
c6cb46440bdfd_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
c6cb417e55187_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
c6cb46be68f57_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
c6cb431d75aae_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
c6cb470c9a6e5_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
c6cb4162416a1_GRCh38_full_analysis_set_plus_decoy_hla.fa added
c6cb4797061f9_GRCh38.primary_assembly.genome.fa.fai added
c6cb413c771a2_GRCh38.primary_assembly.genome.fa.amb added
c6cb4550e673a_GRCh38.primary_assembly.genome.fa.ann added
c6cb448767830_GRCh38.primary_assembly.genome.fa.bwt added
c6cb429320bc2_GRCh38.primary_assembly.genome.fa.pac added
c6cb411aba155_GRCh38.primary_assembly.genome.fa.sa added
c6cb46df6f9e9_GRCh38.primary_assembly.genome.fa added
c6cb4500bffc7_hs37d5.fa.fai added
c6cb441765df2_hs37d5.fa.amb added
c6cb41cdb809c_hs37d5.fa.ann added
c6cb4bad1ceb_hs37d5.fa.bwt added
c6cb4aa19713_hs37d5.fa.pac added
c6cb41d70ee0d_hs37d5.fa.sa added
c6cb42a5896ee_hs37d5.fa added
c6cb467defa4c_complete_ref_lens.bin added
c6cb450181c9a_ctable.bin added
c6cb427d15618_ctg_offsets.bin added
c6cb46f39cd8b_duplicate_clusters.tsv added
c6cb436bc22ce_info.json added
c6cb4190cb2d_mphf.bin added
c6cb42484ae58_pos.bin added
c6cb44f634cf5_pre_indexing.log added
c6cb44568b2a3_rank.bin added
c6cb414db1c42_ref_indexing.log added
c6cb42f1b6c15_refAccumLengths.bin added
c6cb429a970a0_reflengths.bin added
c6cb42cc06dc9_refseq.bin added
c6cb41b01fb6d_seq.bin added
c6cb45b80cb4e_versionInfo.json added
c6cb41d8a14ae_salmon_index added
c6cb43126120e_chrLength.txt added
c6cb454f12d48_chrName.txt added
c6cb431518650_chrNameLength.txt added
c6cb46347949_chrStart.txt added
c6cb41d67a578_exonGeTrInfo.tab added
c6cb45a839212_exonInfo.tab added
c6cb417e01a9e_geneInfo.tab added
c6cb4b5e9f61_Genome added
c6cb42a8f91d9_genomeParameters.txt added
c6cb459567891_Log.out added
c6cb4283a1ffd_SA added
c6cb4363caec5_SAindex added
c6cb463f80fa4_sjdbInfo.txt added
c6cb445ab0e0a_sjdbList.fromGTF.out.tab added
c6cb4609545b3_sjdbList.out.tab added
c6cb44bd709f0_transcriptInfo.tab added
c6cb415c32aa4_GRCh38.GENCODE.v42_100 added
c6cb48669bcc_knownGene_hg38.sql added
c6cb43b10d77b_knownGene_hg38.txt added
c6cb44c7f4d72_refGene_hg38.sql added
c6cb49f766f9_refGene_hg38.txt added
c6cb45f9585d4_knownGene_mm39.sql added
c6cb41be29a67_knownGene_mm39.txt added
c6cb44f60199d_refGene_mm39.sql added
c6cb47470a216_refGene_mm39.txt added
trying URL 'https://storage.googleapis.com/reusedata/echo/outfile.txt'
Content type 'text/plain' length 30 bytes
==================================================
downloaded 30 bytes
trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.yml'
Content type 'application/x-yaml' length 151 bytes
==================================================
downloaded 151 bytes
trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.cwl'
Content type 'application/octet-stream' length 1152 bytes
==================================================
downloaded 1152 bytes
trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.md5'
Content type 'application/octet-stream' length 45 bytes
==================================================
downloaded 45 bytes
trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.sh'
Content type 'application/x-shellscript' length 68 bytes
==================================================
downloaded 68 bytes
Data is downloaded:
/tmp/RtmpwcxqJ6/test_gcpData/outfile.txt
}[1;30mINFO[0m Final process status is success
NOTE: existing caches will be removed and regenerated!
Updating recipes...
STAR_index.R added
bowtie2_index.R added
echo_out.R added
ensembl_liftover.R added
gcp_broad_gatk_hg19.R added
gcp_broad_gatk_hg38.R added
gcp_gatk_mutect2_b37.R added
gcp_gatk_mutect2_hg38.R added
gencode_annotation.R added
gencode_genome_grch38.R added
gencode_transcripts.R added
hisat2_index.R added
reference_genome.R added
salmon_index.R added
ucsc_database.R added
Data recipe loaded!
Use inputs(ensembl_liftover) to check required input parameters before evaluation.
Check here: https://rcwl.org/dataRecipes/ensembl_liftover.html
for user instructions (e.g., eligible input values, data source, etc.)
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 44 ]
> Sys.setenv(cachePath = file.path(tempdir(), "cache"))
>
>
>
> proc.time()
user system elapsed
18.228 1.056 20.108
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 5.992 | 0.346 | 6.338 | |
| dataSearch | 1.179 | 0.030 | 1.211 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.844 | 0.080 | 5.261 | |
| getData | 0.001 | 0.000 | 0.000 | |
| meta_data | 0.001 | 0.000 | 0.000 | |
| recipeHub-class | 0.122 | 0.003 | 0.125 | |
| recipeLoad | 1.295 | 0.027 | 1.323 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.595 | 0.008 | 0.605 | |
| recipeUpdate | 0 | 0 | 0 | |